Lecture 29 Regulation of Gene Expression Flashcards
1
Q
Linkage analysis
A
- could take years
- looked at X-chromosomes and autosomes because they undergo recombination
- Y chromosome does not undergo recombination
2
Q
Exome sequencing
A
- allows us to identify causal mutations in those cases where a large family suitable for linkage analysis is not available
- only takes a couple of individuals
- relatively inexpensive (few thousand dollars)
3
Q
Gene nomenclature
A
- all letters in the gene are italicized
- human gene names are designated with capitalized and italicized letters
- Mouse genes are designated with the 1st letter capitalized and all letters italicized
- LRP5 vs Lrp5(mouse)
4
Q
DNA sequencing
A
- genome sequencing
- exons
- mRNA (transcriptomic sequencing or RNA-seq)
- Epigenomics
5
Q
Genome sequencing
A
- every base in the human genome or mouse
- putting it in correct order
6
Q
Exomic
A
- only on exons or protein coding information
7
Q
mRNA sequencing
A
- messenger RNA population in different tissues
- which genes are being expressed at that time of extraction
8
Q
Epigenomics
A
- DNA methylation
- ChIP sequencing
- Ribosome profiling
9
Q
cost of DNA sequencing
A
- becoming more and more affordable
10
Q
Important questions in regulation of gene expression?
A
- how is the DNA sequence information read by the cell
- What is the relationship between the start site of transcription and the location of the control sequences?
11
Q
Whats a gene?
A
- A gene is defined as a segment of DNA that is transcribed into RNA and its associated transcriptional control regions
- Not just the information that gives rise to the protein, its the exons, introns, and untranslated regions and transcriptional control regions
12
Q
Levels of gene expression control
A
- gene requirements
- gene specific requirements
13
Q
Gene requirements
A
- transcriptional machinery (must be present for transcription to occur)
14
Q
Gene specific requirements
A
- intracellular hormone- receptor complexes
(steroids (estrogen, testosterone, Vit D3 etc.) and their cognate receptors) - Intracellular second messengers
(peptide hormones that bind to cell membrane receptors) - Gene specific (class specific) transcription factors
- Gene regulatory sequences
15
Q
DNA Binding protein Motifs
A
- Helix-loop- helix
- Helix- turn-helix
- Leucine Zipper
16
Q
Helix-loop-helix
A
- common in transcription factors and consists of alpha helices bound by a looping stretch of amino acids
17
Q
Zinc Finger Motifs
A
- multiple types but all have a bound zinc metal ion associated with the protein. Some have an alpha helix plus beta sheet structure, others have a more helix turn helix structure. Can be monomers or dimers
18
Q
Helix-turn-helix
A
- DNA binding motif consisting of two alpha helices joined by a short stretch of amino acids
19
Q
Leucine zipper
A
- two proteins each with an alpha helix form a Y shaped coiled-coil structure. Results in both protein and DNA binding
20
Q
Important DNA sequences in Pol II transcribed genes
A
- TATA box
- INR
- DPE
- BRE
21
Q
TATA box
A
- located ~ 25-30 bp 5’ of the start site of transcripts
- binds to the TBP subunit of TFIID
22
Q
INR
A
- contains start site of transcription for many RNA Pol II genes, binds TFIID
23
Q
DPE
A
- located at +30 (3’) of the start site
- binds TFIID
24
Q
BRE:
A
- located at -35 (5’) of the start site,
- Binds TFIIB
25
Is DNA a rigid linear structure
- no DNA can loop back on itself
| - why regulatory proteins can be far away from the start site (but close in 3D)
26
Summary of activation of Transcription at a specific promoter
1. Gene activator protein binds to chromatin
2. Chromatin Remodeling
3. Covalent histone modification
4. Additional activator proteins bound to gene regulatory region
5. Assembly of pre-initiation complex at the promoter
6. Transcription initiation
27
Multiple levels of control of Eukaryotic gene expression, why is it neccessary?
- necessary so gene is only expressed when you need it and protein is only made when you need it
28
What are the different methods of regulating gene expression/transcription?
- Transcriptional control
- RNA processing control
- RNA transport and localization control
- Translation control
- mRNA degradation control (miRNA)
- Protein activity control
29
What 5 families/pathways work together to turn a fertilized egg into a human?
1. Receptor Tyrosine Kinase
2. TGFB superfamily
3. Wnt
4. Hedgehog
5. Notch
30
Why are B-cattenin levels low in the cell?
- because they signal many growth pathways
31
How are B cat levels low?
- degredation complex
32
What happens when wnt is present?
- B cat is no longer degreaded and it can translocate into the nucleus and binds to TCF (which is bound to the DNA)
33
Mutation in wnt/B-catenin pathway can lead to what?
-cancer
34
Dkk1
- binds to Lrp5/6 which gets it degraded so wnt can function
35
Sclerostin
-binds to Lrp5/6 which prevents wnt from binding
36
Frizzled
-homologs which bind to wnt so it cant bind to the Lrp5/6
37
Wise
- binds to Lrp6
